# HG changeset patch
# User nikos
# Date 1405423186 14400
# Node ID 558f7f9baa78b3bb34796c4f687a65610b98554b
# Parent  998c98233c36b917251b016c91ed3a856ffc4047
Uploaded

diff -r 998c98233c36 -r 558f7f9baa78 make_ucsc_track.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/make_ucsc_track.xml	Tue Jul 15 07:19:46 2014 -0400
@@ -0,0 +1,34 @@
+<tool id="make_ucsc_track" name="UCSC Track Line">
+  <description> Create a track line to import a bigWig or bigBed file in the UCSC genome browser </description>
+  <command interpreter="bash"> 
+	make_ucsc_track.sh -i $input -t ${input.ext} -n '$name' -o $assembly > $output
+  </command>
+  <inputs>
+    <param name="input" type="data" format="bigwig,bigbed" label="Input file" help="bigWig or bigBEd format." />
+    <param name="name" type="text" label="Track name" help="Type the track name you want to appear when you import the file in the UCSC browser." >
+         <validator type="empty_field" />
+    </param>
+
+    <param name="assembly" type="text" label="Orgamism assembly" help="E.g. hg19" >
+	<validator type="empty_field" />
+    </param>
+
+<!--    <param name="visibility" type="select" label="Track visibility">
+	<option value="3">Full</option>
+        <option value="2">Pack</option>
+        <option value="1">Dense</option>
+    </param>
+-->
+  </inputs>
+  
+  <outputs>
+    <data format="txt" name="output"/> 
+  </outputs>
+  <help>
+This tool creates a UCSC track line for a bigWig or bigBed dataset in Galaxy. The text output can be pasted in the "Paste URLs or data" form in the `Add Custom Tracks`_ section of the UCSC Genome Browser.
+
+.. _Add Custom Tracks: http://genome.ucsc.edu/cgi-bin/hgCustom 
+
+  </help>
+</tool>
+